Mercurial > repos > tduigou > seq_to_db
diff output.json @ 0:178d068648f4 draft
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
| author | tduigou |
|---|---|
| date | Thu, 12 Jun 2025 08:27:18 +0000 |
| parents | |
| children | 5db1c2b9edb8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output.json Thu Jun 12 08:27:18 2025 +0000 @@ -0,0 +1,627 @@ +{ + "summary": { + "num_errors": 0, + "num_failures": 3, + "num_skips": 0, + "num_tests": 4 + }, + "tests": [ + { + "data": { + "inputs": { + "adv|execution_enable": false, + "annotation_column": "annotation", + "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "fragment_column": "fragment", + "genbank_files": { + "id": "d1dc40ebed860870", + "src": "hdca" + }, + "sequence_column": "sequence", + "table": "sample" + }, + "job": { + "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/8/6/d/dataset_86d5129f-932a-4577-895e-245fe4d628fc.dat,/tmp/tmphs5lamwi/files/5/d/a/dataset_5dae2e32-d3f9-4f9b-9732-e6e2d297c2a7.dat,/tmp/tmphs5lamwi/files/0/9/a/dataset_09a835e8-673b-43e3-9bb3-f51c3a727f59.dat,/tmp/tmphs5lamwi/files/3/3/7/dataset_337d084d-9ace-4611-ac83-5ad372068c7f.dat,/tmp/tmphs5lamwi/files/6/f/2/dataset_6f2d701c-7b19-4604-a1ee-a74bd2a57870.dat' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output '/tmp/tmphs5lamwi/job_working_directory/000/6/outputs/dataset_18f1dadc-56f5-4df2-beeb-04c270bb1b29.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/8/6/d/dataset_86d5129f-932a-4577-895e-245fe4d628fc.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/5/d/a/dataset_5dae2e32-d3f9-4f9b-9732-e6e2d297c2a7.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/0/9/a/dataset_09a835e8-673b-43e3-9bb3-f51c3a727f59.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/3/3/7/dataset_337d084d-9ace-4611-ac83-5ad372068c7f.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/6/f/2/dataset_6f2d701c-7b19-4604-a1ee-a74bd2a57870.dat:HC_Amp_ccdB.gb' --json_conf 'None' --execution_enable 'false'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-06-12T08:11:40.445752", + "dependencies": [], + "exit_code": 0, + "external_id": "126337", + "galaxy_version": "24.2", + "handler": null, + "history_id": "d1dc40ebed860870", + "id": "9b05862cf50a24d4", + "inputs": { + "genbank_files1": { + "id": "d1dc40ebed860870", + "src": "hda", + "uuid": "86d5129f-932a-4577-895e-245fe4d628fc" + }, + "genbank_files2": { + "id": "8a8d0bbb0c3dafa4", + 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"\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", + "dbkey": "\"?\"", + "fragment_column": "\"fragment\"", + "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", + "sequence_column": "\"sequence\"", + "table": "\"sample\"" + }, + "state": "ok", + "stderr": "", + "stdout": "Execution disabled because sequence_column is set to 'false'.\n", + "tool_id": "seq_to_db", + "tool_stderr": "", + "tool_stdout": "Execution disabled because sequence_column is set to 'false'.\n", + "update_time": "2025-06-12T08:11:46.862307", + "user_email": "planemo@galaxyproject.org", + "user_id": "d1dc40ebed860870" + }, + "output_problems": [ + "Output output: different than expected\nExpected 5+-0 lines in the output found 0" + ], + "status": "failure", + "test_index": 0, + "time_seconds": 26.20578122138977, + "tool_id": "seq_to_db", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "seq_to_db-0" + }, + { + "data": { + "inputs": { + "adv|json_conf": { + "id": 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'/tmp/tmphs5lamwi/files/2/b/e/dataset_2be2db07-173c-45ff-94a0-3461122df268.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/f/1/5/dataset_f1590ccd-1d12-4f95-98b0-fcc4b2cbc80e.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/8/c/2/dataset_8c22a014-8cf2-4575-ae96-c85556a689fb.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/7/f/b/dataset_7fb30eee-10c8-4d84-932e-28f674b1dfc4.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/4/f/b/dataset_4fb6ab60-c194-420f-b10f-de2aa2086638.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmphs5lamwi/files/d/0/0/dataset_d00d7320-cfff-4799-af9d-476da677e0c1.dat' --execution_enable 'true'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-06-12T08:12:07.955341", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pandas", + "version": "2.2.3" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "sqlalchemy", + "version": "2.0.40" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "psycopg2", + "version": "2.9.9" + } + ], + "exit_code": 0, + "external_id": "126847", + "galaxy_version": "24.2", + "handler": null, + "history_id": "8a8d0bbb0c3dafa4", + "id": "e932b28e673f61fd", + "inputs": { + "adv|json_conf": { + "id": "faf36c8bb3bbf1fc", + "src": 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"\"input\"", + "adv": "{\"execution_enable\": true, \"json_conf\": {\"values\": [{\"id\": 12, \"src\": \"hda\"}]}}", + "annotation_column": null, + "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": null, + "dbkey": "\"?\"", + "fragment_column": null, + "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}", + "sequence_column": null, + "table": null + }, + "state": "ok", + "stderr": "", + "stdout": "Execution was blocked by config (execution = false)\n", + "tool_id": "seq_to_db", + "tool_stderr": "", + "tool_stdout": "Execution was blocked by config (execution = false)\n", + "update_time": "2025-06-12T08:12:14.967090", + "user_email": "planemo@galaxyproject.org", + "user_id": "d1dc40ebed860870" + }, + "output_problems": [ + "Output output: different than expected\nExpected 5+-0 lines in the output found 0" + ], + "status": "failure", + "test_index": 1, + "time_seconds": 28.067287921905518, + "tool_id": "seq_to_db", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "seq_to_db-1" + }, + { + "data": { + "inputs": { + "annotation_column": "annotation", + "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "fragment_column": "fragment", + "genbank_files": { + "id": "bf0fa404613c4f02", + "src": "hdca" + }, + "sequence_column": "sequence", + "table": "sample" + }, + "job": { + "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/1/5/a/dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat,/tmp/tmphs5lamwi/files/0/2/6/dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat,/tmp/tmphs5lamwi/files/0/6/a/dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat,/tmp/tmphs5lamwi/files/5/7/a/dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat,/tmp/tmphs5lamwi/files/2/a/a/dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output '/tmp/tmphs5lamwi/job_working_directory/000/19/outputs/dataset_168a000a-8805-4f1d-918e-4ebbd60fd654.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/1/5/a/dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/0/2/6/dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/0/6/a/dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/5/7/a/dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/2/a/a/dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat:HC_Amp_ccdB.gb' --json_conf 'None' --execution_enable 'true'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-06-12T08:12:35.708354", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pandas", + "version": "2.2.3" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "sqlalchemy", + "version": "2.0.40" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "psycopg2", + "version": "2.9.9" + } + ], + "exit_code": 0, + "external_id": "127455", + "galaxy_version": "24.2", + "handler": null, + "history_id": "bf0fa404613c4f02", + "id": "48ac62a10b51b648", + "inputs": { + "genbank_files1": { + "id": "9863db5e96bd9ae2", + "src": "hda", + "uuid": "15a3a402-8761-43db-81ae-e4bb3f2d41d8" + }, + "genbank_files2": { + "id": "c55450b682f38454", + "src": "hda", + "uuid": "02636863-d06d-46bb-bcd3-c22b162ad92c" + }, + "genbank_files3": { + "id": "b2f6887fdac0a65b", + "src": "hda", + "uuid": "06a85205-3621-425b-8eca-56f44a3ceaed" + }, + "genbank_files4": { + "id": "f5829ca36951d902", + "src": "hda", + "uuid": "57afe769-fe76-4890-9c62-c2014ecf8529" + }, + "genbank_files5": { + "id": "baef710e55d31add", + "src": "hda", + "uuid": "2aaaf350-bb2f-4390-81e3-6eeeaae0481e" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output": { + "id": "48ac62a10b51b648", + "src": "hda", + "uuid": "168a000a-8805-4f1d-918e-4ebbd60fd654" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"execution_enable\": true, \"json_conf\": null}", + "annotation_column": "\"annotation\"", + "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", + "dbkey": "\"?\"", + "fragment_column": "\"fragment\"", + "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", + "sequence_column": "\"sequence\"", + "table": "\"sample\"" + }, + "state": "ok", + "stderr": "", + "stdout": "Connected to database.\nProcessing file: dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat(p6_Kozak-ATG)\nProcessing file: dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmphs5lamwi/job_working_directory/000/19/outputs/dataset_168a000a-8805-4f1d-918e-4ebbd60fd654.dat'.\n", + "tool_id": "seq_to_db", + "tool_stderr": "", + "tool_stdout": "Connected to database.\nProcessing file: dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat(p6_Kozak-ATG)\nProcessing file: dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmphs5lamwi/job_working_directory/000/19/outputs/dataset_168a000a-8805-4f1d-918e-4ebbd60fd654.dat'.\n", + "update_time": "2025-06-12T08:12:41.972140", + "user_email": "planemo@galaxyproject.org", + "user_id": "d1dc40ebed860870" + }, + "status": "success", + "test_index": 2, + "time_seconds": 27.17548680305481, + "tool_id": "seq_to_db", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "seq_to_db-2" + }, + { + "data": { + "inputs": { + "adv|json_conf": { + "id": "81096e298c6cd33b", + "src": "hda" + }, + "genbank_files": { + "id": "f71740853e0eea8f", + "src": "hdca" + } + }, + "job": { + "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/7/7/d/dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat,/tmp/tmphs5lamwi/files/5/1/a/dataset_51ae04ed-e634-4f46-ae13-0ce31dbacc37.dat,/tmp/tmphs5lamwi/files/c/6/4/dataset_c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9.dat,/tmp/tmphs5lamwi/files/e/f/7/dataset_ef7a853c-dc0e-47dc-bf52-6f45291358b1.dat,/tmp/tmphs5lamwi/files/1/3/a/dataset_13a4680c-d654-45d9-bdab-75dca91c36da.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmphs5lamwi/job_working_directory/000/26/outputs/dataset_431acc98-f2ee-4e32-876a-33ef788c7eeb.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/7/7/d/dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/5/1/a/dataset_51ae04ed-e634-4f46-ae13-0ce31dbacc37.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/c/6/4/dataset_c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/e/f/7/dataset_ef7a853c-dc0e-47dc-bf52-6f45291358b1.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/1/3/a/dataset_13a4680c-d654-45d9-bdab-75dca91c36da.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmphs5lamwi/files/1/6/8/dataset_1681d2f4-591b-48a4-a469-0b6d9d29897b.dat' --execution_enable 'true'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-06-12T08:13:02.907605", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pandas", + "version": "2.2.3" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "sqlalchemy", + "version": "2.0.40" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "psycopg2", + "version": "2.9.9" + } + ], + "exit_code": 1, + "external_id": "127952", + "galaxy_version": "24.2", + "handler": null, + "history_id": "f71740853e0eea8f", + "id": "ae7479dd630bf125", + "inputs": { + "adv|json_conf": { + "id": "81096e298c6cd33b", + "src": "hda", + "uuid": "1681d2f4-591b-48a4-a469-0b6d9d29897b" + }, + "genbank_files1": { + "id": "4bb85627388cf8ba", + "src": "hda", + "uuid": "77d5679d-4fb4-4b27-afe7-930f4b3d6076" + }, + "genbank_files2": { + "id": "00078d50fa80d7bb", + "src": "hda", + "uuid": "51ae04ed-e634-4f46-ae13-0ce31dbacc37" + }, + "genbank_files3": { + "id": "221d11c5cc4eab13", + "src": "hda", + "uuid": "c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9" + }, + "genbank_files4": { + "id": "bc838ca4b455c7c4", + "src": "hda", + "uuid": "ef7a853c-dc0e-47dc-bf52-6f45291358b1" + }, + "genbank_files5": { + "id": "04052285d124af02", + "src": "hda", + "uuid": "13a4680c-d654-45d9-bdab-75dca91c36da" + } + }, + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 1 ()", + "error_level": 3, + "exit_code": 1, + "type": "exit_code" + } + ], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output": { + "id": "ae7479dd630bf125", + "src": "hda", + "uuid": "431acc98-f2ee-4e32-876a-33ef788c7eeb" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"execution_enable\": true, \"json_conf\": {\"values\": [{\"id\": 25, \"src\": \"hda\"}]}}", + "annotation_column": null, + "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": null, + "dbkey": "\"?\"", + "fragment_column": null, + "genbank_files": "{\"values\": [{\"id\": 4, \"src\": \"hdca\"}]}", + "sequence_column": null, + "table": null + }, + "state": "error", + "stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n", + "stdout": "Connected to database.\nProcessing file: dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat(p7_L7Ae-Weiss)\nError during GB file insertion: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n", + "tool_id": "seq_to_db", + "tool_stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n", + "tool_stdout": "Connected to database.\nProcessing file: dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat(p7_L7Ae-Weiss)\nError during GB file insertion: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n", + "update_time": "2025-06-12T08:13:09.078361", + "user_email": "planemo@galaxyproject.org", + "user_id": "d1dc40ebed860870" + }, + "output_problems": [ + "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n.", + "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n." + ], + "status": "failure", + "test_index": 3, + "time_seconds": 26.706940174102783, + "tool_id": "seq_to_db", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "seq_to_db-3" + } + ], + "version": "0.1" +} \ No newline at end of file